A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/ampliseq analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2025-01-21, 15:49 CET
based on data in:
/cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work/f8/db336f000bc9a1e31493199e593079
General Statistics
| Sample Name | Trimmed bases |
|---|---|
| sampleID_1 | 14.9% |
| sampleID_1a | 16.1% |
| sampleID_2 | 11.1% |
| sampleID_2a | 15.3% |
Cutadapt
Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Trimmed Sequence Lengths (5')
This plot shows the number of reads with certain lengths of adapter trimmed for the 5' end.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
nf-core/ampliseq Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/ampliseq
Methods
Data was processed using nf-core/ampliseq v2.13.0dev (doi: 10.5281/zenodo.1493841), (doi: 10.3389/fmicb.2020.550420) (Straub et al., 2020) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.3 (Di Tommaso et al., 2017) with the following command:
nextflow -quiet -log /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/nextflow.log run /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/main.nf -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/nextflow.config -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/nextflow.config -params-file /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/params.json -ansi-log false -profile test_pplace_hmmsearch,singularity -with-trace /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/trace.csv -w /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work
References
- Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front Microbiol. 2020 Oct 23;11:550420. https://doi.org/10.3389/fmicb.2020.550420
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/ampliseq Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/ampliseq
Main arguments
- FW_primer
- GTGYCAGCMGCCGCGGTAA
- RV_primer
- GGACTACNVGGGTWTCTAAT
- input
- https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv
- metadata
- https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata.tsv
- outdir
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/output
ASV post processing
- filter_ssu
- bac
Taxonomic database
- qiime_ref_taxonomy
- greengenes85
ASV filtering
- min_frequency
- 10
- min_samples
- 2
Downstream analysis
- tax_agglom_max
- 3
- tax_agglom_min
- 1
Differential abundance analysis
- ancombc_effect_size
- 1
Pipeline summary report
- report_css
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/nf-core_style.css
- report_logo
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/nf-core-ampliseq_logo_light_long.png
- report_template
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/report_template.Rmd
Skipping specific steps
- skip_alpha_rarefaction
- true
- skip_dada_taxonomy
- true
- skip_fastqc
- true
- skip_qiime
- true
Institutional config options
- config_profile_description
- Minimal test dataset to check pipeline function
- config_profile_name
- Test profile
Other parameters
- pplace_sheet
- https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/phyloplace/testdata/phylosearch_input.csv
Core Nextflow options
- configFiles
- N/A
- containerEngine
- singularity
- launchDir
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a
- profile
- test_pplace_hmmsearch,singularity
- projectDir
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq
- runName
- mighty_gates
- userName
- ddl
- workDir
- /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work